First, load the libraries needed for the workflow
library(tidyverse)
library(CoRC)
Put in all variables needed to customise the workflow
Put in the path to the model (SBML), as url or local path (as string) and load the model. Use loadModel() for .cps models.
modelPathSBML <- "./Models/Leloup2004Circadian_model.xml"
loadSBML(modelPathSBML)
#> # A COPASI model reference:
#> Model name: "Leloup2004 - Mammalian Circadian Rhythm models for 23.8 and 24.2 hours timeperiod"
#> Number of compartments: 1
#> Number of species: 19
#> Number of reactions: 48
Load the data into the variable data.
data <- read.csv("./Data/Leloup2004Circadian_data.csv", sep = "")
Define experiment(s) for Parameter Estimation. For multiple experiments use list of defineExperiments().
experiment <- defineExperiments(
data = data,
type = c("time", "dependent", "dependent", "dependent", "dependent", "dependent", "dependent"),
mapping = c(NA, getSpeciesReferences(key = c("MP", "MC", "MB", "PTot", "CTot", "BTot"))$concentration),
weight_method = "mean_square"
)
Set Parameter Estimation Parameters. For more parameters, copy the defineParameterEstimationParameter() function and append the list. All parameters in this model are mapped to global Quantities. For Parameter Estimation, the Global Quantities not assigned or with an ode (so only “fixed” global Quantities) are estimated.
globalQ <- getGlobalQuantities()[getGlobalQuantities()$type == "fixed",]$key
lapply(globalQ, add_pe_param_global, lower = 100, upper = 100)
#> [[1]]
#> NULL
#>
#> [[2]]
#> NULL
#>
#> [[3]]
#> NULL
#>
#> [[4]]
#> NULL
#>
#> [[5]]
#> NULL
#>
#> [[6]]
#> NULL
#>
#> [[7]]
#> NULL
#>
#> [[8]]
#> NULL
#>
#> [[9]]
#> NULL
#>
#> [[10]]
#> NULL
#>
#> [[11]]
#> NULL
#>
#> [[12]]
#> NULL
#>
#> [[13]]
#> NULL
#>
#> [[14]]
#> NULL
#>
#> [[15]]
#> NULL
#>
#> [[16]]
#> NULL
#>
#> [[17]]
#> NULL
#>
#> [[18]]
#> NULL
#>
#> [[19]]
#> NULL
#>
#> [[20]]
#> NULL
#>
#> [[21]]
#> NULL
#>
#> [[22]]
#> NULL
#>
#> [[23]]
#> NULL
#>
#> [[24]]
#> NULL
#>
#> [[25]]
#> NULL
#>
#> [[26]]
#> NULL
#>
#> [[27]]
#> NULL
#>
#> [[28]]
#> NULL
#>
#> [[29]]
#> NULL
#>
#> [[30]]
#> NULL
#>
#> [[31]]
#> NULL
#>
#> [[32]]
#> NULL
#>
#> [[33]]
#> NULL
#>
#> [[34]]
#> NULL
#>
#> [[35]]
#> NULL
#>
#> [[36]]
#> NULL
#>
#> [[37]]
#> NULL
#>
#> [[38]]
#> NULL
#>
#> [[39]]
#> NULL
#>
#> [[40]]
#> NULL
#>
#> [[41]]
#> NULL
#>
#> [[42]]
#> NULL
#>
#> [[43]]
#> NULL
#>
#> [[44]]
#> NULL
#>
#> [[45]]
#> NULL
#>
#> [[46]]
#> NULL
Set Parameter Estimation Settings.
setParameterEstimationSettings(
method = "LevenbergMarquardt"
)
Set Sigma Point Method Settings. Choose alpha, beta, kappa, and the measurement error (var)
alpha <- 1
beta <- 2
kappa <- 0
measurement_error <- 0.05
Do you want to save the result as a RDS object? Also give the file, where you want to save it.
save <- TRUE
file <- "docs/SP_Leloup"
This should generally not need to be changed, only if the workflow is to be changed more generally.
result <-
runSigmaPoint(
alpha = alpha,
beta = beta,
kappa = kappa,
var = measurement_error,
experiments = experiment,
mean_fit_as_basis = TRUE,
)
if (save){
saveRDS(result,
file = file)
}
This workflow produces the following output:
result$sp_mean
#> Values[vmP].InitialValue Values[kdmp].InitialValue Values[KAP].InitialValue
#> 1.101504744 0.003451218 0.714878225
#> Values[KmP].InitialValue Values[vmC].InitialValue Values[kdmc].InitialValue
#> 0.365326811 0.990230227 0.011315345
#> Values[KAC].InitialValue Values[KmC].InitialValue Values[vmB].InitialValue
#> 0.587155824 0.427851568 0.768961853
#> Values[kdmb].InitialValue Values[KIB].InitialValue Values[KmB].InitialValue
#> 0.007101126 2.164843436 0.841746130
#> Values[k1].InitialValue Values[k2].InitialValue Values[k3].InitialValue
#> 0.431505382 0.200771061 0.293499161
#> Values[k4].InitialValue Values[k5].InitialValue Values[k6].InitialValue
#> 0.210254502 0.385797339 0.187131010
#> Values[k7].InitialValue Values[k8].InitialValue Values[kdnc].InitialValue
#> 0.790218122 0.313895046 0.132251954
#> Values[kdn].InitialValue Values[kstot].InitialValue Values[m].InitialValue
#> 0.004577419 0.997737634 1.483688042
#> Values[n].InitialValue Values[vstot].InitialValue Values[Kd].InitialValue
#> 6.880430384 0.972988762 0.281510483
#> Values[Kdp].InitialValue Values[Kp].InitialValue Values[Vphos].InitialValue
#> 0.217435602 0.106819657 0.406600990
#> Values[V1B].InitialValue Values[V1C].InitialValue Values[V2B].InitialValue
#> 0.525223406 0.468599275 0.108969896
#> Values[V2C].InitialValue Values[V2P].InitialValue Values[V2PC].InitialValue
#> -0.044763959 0.304847956 0.166897312
#> Values[V3B].InitialValue Values[V4B].InitialValue Values[V4PC].InitialValue
#> 0.439097722 0.236139676 0.245730456
#> Values[vdBC].InitialValue Values[vdBN].InitialValue Values[vdCC].InitialValue
#> -0.102842238 0.712961988 0.797071944
#> Values[vdIN].InitialValue Values[vdPC].InitialValue Values[vdPCC].InitialValue
#> 1.619296051 0.711853066 0.583241870
#> Values[vdPCN].InitialValue
#> 1.426045246
result$sp_cov_matrix
#> Values[vmP].InitialValue Values[kdmp].InitialValue
#> Values[vmP].InitialValue 1.640030e-03 0.0001967238
#> Values[kdmp].InitialValue 1.967238e-04 0.0005644759
#> Values[KAP].InitialValue -4.771169e-04 -0.0005700953
#> Values[KmP].InitialValue -4.674045e-03 -0.0048999256
#> Values[vmC].InitialValue 7.788995e-04 0.0013369198
#> Values[kdmc].InitialValue 5.951593e-04 0.0004578829
#> Values[KAC].InitialValue 2.928525e-04 -0.0001348343
#> Values[KmC].InitialValue -1.734717e-03 -0.0019300259
#> Values[vmB].InitialValue 1.707357e-03 0.0022244241
#> Values[kdmb].InitialValue 1.107572e-04 0.0001656489
#> Values[KIB].InitialValue 8.899279e-03 0.0129312552
#> Values[KmB].InitialValue -3.103139e-02 -0.0378921558
#> Values[k1].InitialValue -3.385650e-04 0.0001647050
#> Values[k2].InitialValue -4.743382e-03 -0.0063010067
#> Values[k3].InitialValue 3.738589e-03 0.0039002896
#> Values[k4].InitialValue 6.542612e-04 0.0011626005
#> Values[k5].InitialValue 7.276377e-04 0.0008645500
#> Values[k6].InitialValue 2.939448e-04 0.0006283965
#> Values[k7].InitialValue -1.759883e-02 -0.0240077444
#> Values[k8].InitialValue -7.179371e-03 -0.0154549988
#> Values[kdnc].InitialValue -3.901189e-04 -0.0004725572
#> Values[KAP].InitialValue Values[KmP].InitialValue
#> Values[vmP].InitialValue -0.0004771169 -0.0046740452
#> Values[kdmp].InitialValue -0.0005700953 -0.0048999256
#> Values[KAP].InitialValue 0.0029027577 0.0065751012
#> Values[KmP].InitialValue 0.0065751012 0.0694482114
#> Values[vmC].InitialValue -0.0014281400 -0.0142958878
#> Values[kdmc].InitialValue -0.0005814399 -0.0057138134
#> Values[KAC].InitialValue 0.0010220657 -0.0020026852
#> Values[KmC].InitialValue 0.0008359858 0.0208143406
#> Values[vmB].InitialValue -0.0026620202 -0.0261898533
#> Values[kdmb].InitialValue -0.0002117754 -0.0019641838
#> Values[KIB].InitialValue -0.0132155660 -0.1520117914
#> Values[KmB].InitialValue 0.0432727595 0.4430988840
#> Values[k1].InitialValue -0.0003730674 0.0005495606
#> Values[k2].InitialValue 0.0089292068 0.0729326016
#> Values[k3].InitialValue -0.0056945050 -0.0529917424
#> Values[k4].InitialValue 0.0006830092 0.0008569212
#> Values[k5].InitialValue -0.0005099632 -0.0108442910
#> Values[k6].InitialValue -0.0008727875 -0.0076190932
#> Values[k7].InitialValue 0.0288730162 0.2792492413
#> Values[k8].InitialValue 0.0192067577 0.1753984341
#> Values[kdnc].InitialValue 0.0005005619 0.0057820606
#> Values[vmC].InitialValue Values[kdmc].InitialValue
#> Values[vmP].InitialValue 0.0007788995 5.951593e-04
#> Values[kdmp].InitialValue 0.0013369198 4.578829e-04
#> Values[KAP].InitialValue -0.0014281400 -5.814399e-04
#> Values[KmP].InitialValue -0.0142958878 -5.713813e-03
#> Values[vmC].InitialValue 0.0038870627 1.173256e-03
#> Values[kdmc].InitialValue 0.0011732564 7.925043e-04
#> Values[KAC].InitialValue -0.0004520536 -1.651658e-05
#> Values[KmC].InitialValue -0.0057532594 -1.239134e-03
#> Values[vmB].InitialValue 0.0059157159 2.403898e-03
#> Values[kdmb].InitialValue 0.0004391074 1.769555e-04
#> Values[KIB].InitialValue 0.0334974941 1.396566e-02
#> Values[KmB].InitialValue -0.1008145359 -4.109984e-02
#> Values[k1].InitialValue 0.0003311778 -2.712440e-04
#> Values[k2].InitialValue -0.0169339838 -6.495013e-03
#> Values[k3].InitialValue 0.0104640979 5.030229e-03
#> Values[k4].InitialValue 0.0032734386 5.988324e-04
#> Values[k5].InitialValue 0.0023848978 9.941486e-04
#> Values[k6].InitialValue 0.0016823887 8.690512e-04
#> Values[k7].InitialValue -0.0638248271 -2.553062e-02
#> Values[k8].InitialValue -0.0392172298 -1.568026e-02
#> Values[kdnc].InitialValue -0.0014278882 -8.103785e-04
#> Values[KAC].InitialValue Values[KmC].InitialValue
#> Values[vmP].InitialValue 2.928525e-04 -0.0017347168
#> Values[kdmp].InitialValue -1.348343e-04 -0.0019300259
#> Values[KAP].InitialValue 1.022066e-03 0.0008359858
#> Values[KmP].InitialValue -2.002685e-03 0.0208143406
#> Values[vmC].InitialValue -4.520536e-04 -0.0057532594
#> Values[kdmc].InitialValue -1.651658e-05 -0.0012391344
#> Values[KAC].InitialValue 2.530224e-03 0.0004808342
#> Values[KmC].InitialValue 4.808342e-04 0.0145154574
#> Values[vmB].InitialValue 9.092004e-06 -0.0092509396
#> Values[kdmb].InitialValue -1.414516e-05 -0.0006875667
#> Values[KIB].InitialValue 1.628013e-03 -0.0520224854
#> Values[KmB].InitialValue -2.201875e-03 0.1574282123
#> Values[k1].InitialValue -7.752998e-04 -0.0006237093
#> Values[k2].InitialValue 1.412651e-03 0.0266045750
#> Values[k3].InitialValue 8.775389e-04 -0.0133784943
#> Values[k4].InitialValue -3.785711e-03 -0.0009726257
#> Values[k5].InitialValue 5.216902e-04 -0.0038542223
#> Values[k6].InitialValue 1.376628e-04 -0.0016151382
#> Values[k7].InitialValue 5.420146e-04 0.0982026580
#> Values[k8].InitialValue 1.549894e-03 0.0572231919
#> Values[kdnc].InitialValue 4.450054e-04 0.0019912999
#> Values[vmB].InitialValue Values[kdmb].InitialValue
#> Values[vmP].InitialValue 1.707357e-03 1.107572e-04
#> Values[kdmp].InitialValue 2.224424e-03 1.656489e-04
#> Values[KAP].InitialValue -2.662020e-03 -2.117754e-04
#> Values[KmP].InitialValue -2.618985e-02 -1.964184e-03
#> Values[vmC].InitialValue 5.915716e-03 4.391074e-04
#> Values[kdmc].InitialValue 2.403898e-03 1.769555e-04
#> Values[KAC].InitialValue 9.092004e-06 -1.414516e-05
#> Values[KmC].InitialValue -9.250940e-03 -6.875667e-04
#> Values[vmB].InitialValue 1.159712e-02 8.710251e-04
#> Values[kdmb].InitialValue 8.710251e-04 6.862704e-05
#> Values[KIB].InitialValue 6.886700e-02 5.088751e-03
#> Values[KmB].InitialValue -1.959841e-01 -1.425939e-02
#> Values[k1].InitialValue 2.361248e-04 2.539470e-05
#> Values[k2].InitialValue -3.227009e-02 -2.428410e-03
#> Values[k3].InitialValue 2.184215e-02 1.640493e-03
#> Values[k4].InitialValue 3.768756e-04 -1.353109e-05
#> Values[k5].InitialValue 4.640330e-03 3.462186e-04
#> Values[k6].InitialValue 3.657756e-03 2.869445e-04
#> Values[k7].InitialValue -1.210570e-01 -9.108611e-03
#> Values[k8].InitialValue -7.566605e-02 -5.750267e-03
#> Values[kdnc].InitialValue -2.465701e-03 -1.863503e-04
#> Values[KIB].InitialValue Values[KmB].InitialValue
#> Values[vmP].InitialValue 0.008899279 -0.031031388
#> Values[kdmp].InitialValue 0.012931255 -0.037892156
#> Values[KAP].InitialValue -0.013215566 0.043272760
#> Values[KmP].InitialValue -0.152011791 0.443098884
#> Values[vmC].InitialValue 0.033497494 -0.100814536
#> Values[kdmc].InitialValue 0.013965658 -0.041099837
#> Values[KAC].InitialValue 0.001628013 -0.002201875
#> Values[KmC].InitialValue -0.052022485 0.157428212
#> Values[vmB].InitialValue 0.068867004 -0.195984067
#> Values[kdmb].InitialValue 0.005088751 -0.014259393
#> Values[KIB].InitialValue 0.577084900 -1.177937453
#> Values[KmB].InitialValue -1.177937453 3.382519408
#> Values[k1].InitialValue 0.004519981 -0.003192034
#> Values[k2].InitialValue -0.176319409 0.545054189
#> Values[k3].InitialValue 0.120589842 -0.369020101
#> Values[k4].InitialValue 0.007425274 -0.011005147
#> Values[k5].InitialValue 0.027918949 -0.078892985
#> Values[k6].InitialValue 0.017483113 -0.059371782
#> Values[k7].InitialValue -0.700540285 2.045841426
#> Values[k8].InitialValue -0.456717185 1.271907004
#> Values[kdnc].InitialValue -0.014862278 0.041556033
#> Values[k1].InitialValue Values[k2].InitialValue
#> Values[vmP].InitialValue -3.385650e-04 -0.0047433822
#> Values[kdmp].InitialValue 1.647050e-04 -0.0063010067
#> Values[KAP].InitialValue -3.730674e-04 0.0089292068
#> Values[KmP].InitialValue 5.495606e-04 0.0729326016
#> Values[vmC].InitialValue 3.311778e-04 -0.0169339838
#> Values[kdmc].InitialValue -2.712440e-04 -0.0064950127
#> Values[KAC].InitialValue -7.752998e-04 0.0014126513
#> Values[KmC].InitialValue -6.237093e-04 0.0266045750
#> Values[vmB].InitialValue 2.361248e-04 -0.0322700894
#> Values[kdmb].InitialValue 2.539470e-05 -0.0024284105
#> Values[KIB].InitialValue 4.519981e-03 -0.1763194091
#> Values[KmB].InitialValue -3.192034e-03 0.5450541889
#> Values[k1].InitialValue 1.784283e-03 -0.0005302363
#> Values[k2].InitialValue -5.302363e-04 0.1040947941
#> Values[k3].InitialValue -6.818670e-04 -0.0628380035
#> Values[k4].InitialValue 3.356606e-03 -0.0064765193
#> Values[k5].InitialValue -2.501045e-04 -0.0124862631
#> Values[k6].InitialValue -3.239268e-04 -0.0095872610
#> Values[k7].InitialValue -3.005106e-03 0.3375970464
#> Values[k8].InitialValue -3.814519e-03 0.2007052367
#> Values[kdnc].InitialValue 3.470799e-04 0.0063203356
#> Values[k3].InitialValue Values[k4].InitialValue
#> Values[vmP].InitialValue 0.0037385894 6.542612e-04
#> Values[kdmp].InitialValue 0.0039002896 1.162600e-03
#> Values[KAP].InitialValue -0.0056945050 6.830092e-04
#> Values[KmP].InitialValue -0.0529917424 8.569212e-04
#> Values[vmC].InitialValue 0.0104640979 3.273439e-03
#> Values[kdmc].InitialValue 0.0050302289 5.988324e-04
#> Values[KAC].InitialValue 0.0008775389 -3.785711e-03
#> Values[KmC].InitialValue -0.0133784943 -9.726257e-04
#> Values[vmB].InitialValue 0.0218421523 3.768756e-04
#> Values[kdmb].InitialValue 0.0016404926 -1.353109e-05
#> Values[KIB].InitialValue 0.1205898419 7.425274e-03
#> Values[KmB].InitialValue -0.3690201005 -1.100515e-02
#> Values[k1].InitialValue -0.0006818670 3.356606e-03
#> Values[k2].InitialValue -0.0628380035 -6.476519e-03
#> Values[k3].InitialValue 0.0544301822 5.014691e-03
#> Values[k4].InitialValue 0.0050146911 1.085884e-01
#> Values[k5].InitialValue 0.0088386021 2.923591e-05
#> Values[k6].InitialValue 0.0071369950 1.659816e-03
#> Values[k7].InitialValue -0.2290995942 6.808221e-03
#> Values[k8].InitialValue -0.1466035433 -8.280477e-03
#> Values[kdnc].InitialValue -0.0047542691 9.313237e-04
#> Values[k5].InitialValue Values[k6].InitialValue
#> Values[vmP].InitialValue 7.276377e-04 2.939448e-04
#> Values[kdmp].InitialValue 8.645500e-04 6.283965e-04
#> Values[KAP].InitialValue -5.099632e-04 -8.727875e-04
#> Values[KmP].InitialValue -1.084429e-02 -7.619093e-03
#> Values[vmC].InitialValue 2.384898e-03 1.682389e-03
#> Values[kdmc].InitialValue 9.941486e-04 8.690512e-04
#> Values[KAC].InitialValue 5.216902e-04 1.376628e-04
#> Values[KmC].InitialValue -3.854222e-03 -1.615138e-03
#> Values[vmB].InitialValue 4.640330e-03 3.657756e-03
#> Values[kdmb].InitialValue 3.462186e-04 2.869445e-04
#> Values[KIB].InitialValue 2.791895e-02 1.748311e-02
#> Values[KmB].InitialValue -7.889298e-02 -5.937178e-02
#> Values[k1].InitialValue -2.501045e-04 -3.239268e-04
#> Values[k2].InitialValue -1.248626e-02 -9.587261e-03
#> Values[k3].InitialValue 8.838602e-03 7.136995e-03
#> Values[k4].InitialValue 2.923591e-05 1.659816e-03
#> Values[k5].InitialValue 2.845808e-03 1.832540e-03
#> Values[k6].InitialValue 1.832540e-03 3.593006e-03
#> Values[k7].InitialValue -4.877440e-02 -3.566099e-02
#> Values[k8].InitialValue -2.872040e-02 -2.257393e-02
#> Values[kdnc].InitialValue -1.055301e-03 -8.675964e-04
#> Values[k7].InitialValue Values[k8].InitialValue
#> Values[vmP].InitialValue -0.0175988320 -0.007179371
#> Values[kdmp].InitialValue -0.0240077444 -0.015454999
#> Values[KAP].InitialValue 0.0288730162 0.019206758
#> Values[KmP].InitialValue 0.2792492413 0.175398434
#> Values[vmC].InitialValue -0.0638248271 -0.039217230
#> Values[kdmc].InitialValue -0.0255306205 -0.015680255
#> Values[KAC].InitialValue 0.0005420146 0.001549894
#> Values[KmC].InitialValue 0.0982026580 0.057223192
#> Values[vmB].InitialValue -0.1210570455 -0.075666051
#> Values[kdmb].InitialValue -0.0091086110 -0.005750267
#> Values[KIB].InitialValue -0.7005402853 -0.456717185
#> Values[KmB].InitialValue 2.0458414257 1.271907004
#> Values[k1].InitialValue -0.0030051062 -0.003814519
#> Values[k2].InitialValue 0.3375970464 0.200705237
#> Values[k3].InitialValue -0.2290995942 -0.146603543
#> Values[k4].InitialValue 0.0068082214 -0.008280477
#> Values[k5].InitialValue -0.0487743984 -0.028720399
#> Values[k6].InitialValue -0.0356609891 -0.022573929
#> Values[k7].InitialValue 1.3089366113 0.826794158
#> Values[k8].InitialValue 0.8267941581 0.727513226
#> Values[kdnc].InitialValue 0.0270928486 0.016196851
#> Values[kdnc].InitialValue Values[kdn].InitialValue
#> Values[vmP].InitialValue -0.0003901189 2.268696e-04
#> Values[kdmp].InitialValue -0.0004725572 2.018907e-04
#> Values[KAP].InitialValue 0.0005005619 -2.210499e-04
#> Values[KmP].InitialValue 0.0057820606 -2.574329e-03
#> Values[vmC].InitialValue -0.0014278882 5.846383e-04
#> Values[kdmc].InitialValue -0.0008103785 2.292922e-04
#> Values[KAC].InitialValue 0.0004450054 3.363037e-05
#> Values[KmC].InitialValue 0.0019912999 -1.006793e-03
#> Values[vmB].InitialValue -0.0024657009 1.067071e-03
#> Values[kdmb].InitialValue -0.0001863503 8.030861e-05
#> Values[KIB].InitialValue -0.0148622785 5.715329e-03
#> Values[KmB].InitialValue 0.0415560326 -1.804661e-02
#> Values[k1].InitialValue 0.0003470799 -3.535087e-05
#> Values[k2].InitialValue 0.0063203356 -3.277567e-03
#> Values[k3].InitialValue -0.0047542691 1.966715e-03
#> Values[k4].InitialValue 0.0009313237 -5.655168e-05
#> Values[k5].InitialValue -0.0010553012 4.701193e-04
#> Values[k6].InitialValue -0.0008675964 2.588697e-04
#> Values[k7].InitialValue 0.0270928486 -1.137009e-02
#> Values[k8].InitialValue 0.0161968509 -6.103530e-03
#> Values[kdnc].InitialValue 0.0015760912 -2.541832e-04
#> Values[kstot].InitialValue Values[m].InitialValue
#> Values[vmP].InitialValue -1.134492e-04 0.0171641143
#> Values[kdmp].InitialValue 3.424773e-04 0.0239330027
#> Values[KAP].InitialValue -3.790871e-04 -0.0271190560
#> Values[KmP].InitialValue -2.863969e-03 -0.2768947382
#> Values[vmC].InitialValue 7.725894e-04 0.0633607015
#> Values[kdmc].InitialValue 1.355702e-04 0.0250347255
#> Values[KAC].InitialValue -1.698914e-05 -0.0007327001
#> Values[KmC].InitialValue -1.371361e-03 -0.1020096675
#> Values[vmB].InitialValue 1.346584e-03 0.1242318825
#> Values[kdmb].InitialValue 9.966793e-05 0.0093543114
#> Values[KIB].InitialValue 8.235181e-03 0.6870023602
#> Values[KmB].InitialValue -2.312244e-02 -2.0936915339
#> Values[k1].InitialValue 9.897290e-05 0.0004038621
#> Values[k2].InitialValue -4.499747e-03 -0.3490293025
#> Values[k3].InitialValue 2.340413e-03 0.2358687793
#> Values[k4].InitialValue -1.540082e-03 0.0085231688
#> Values[k5].InitialValue 8.149080e-04 0.0503432361
#> Values[k6].InitialValue 4.746142e-05 0.0396514221
#> Values[k7].InitialValue -1.593697e-02 -1.2889216477
#> Values[k8].InitialValue -9.686605e-03 -0.8170956473
#> Values[kdnc].InitialValue -6.622050e-05 -0.0258920885
#> Values[n].InitialValue Values[vstot].InitialValue
#> Values[vmP].InitialValue 0.135567981 0.0027712777
#> Values[kdmp].InitialValue 0.082986905 0.0029318068
#> Values[KAP].InitialValue -0.044362578 -0.0034929599
#> Values[KmP].InitialValue -0.870338979 -0.0352946669
#> Values[vmC].InitialValue 0.145481545 0.0080060314
#> Values[kdmc].InitialValue 0.094420549 0.0032746032
#> Values[KAC].InitialValue 0.145750434 0.0001766008
#> Values[KmC].InitialValue -0.237401866 -0.0125797690
#> Values[vmB].InitialValue 0.290836817 0.0151486688
#> Values[kdmb].InitialValue 0.020411368 0.0011284522
#> Values[KIB].InitialValue 2.036780046 0.0838210365
#> Values[KmB].InitialValue -5.191463523 -0.2571825233
#> Values[k1].InitialValue -0.044047924 0.0001595672
#> Values[k2].InitialValue -0.882874781 -0.0429892666
#> Values[k3].InitialValue 0.568458181 0.0290471549
#> Values[k4].InitialValue 1.161392326 0.0006543794
#> Values[k5].InitialValue 0.175740175 0.0061432547
#> Values[k6].InitialValue -0.007318833 0.0047814131
#> Values[k7].InitialValue -3.528843507 -0.1597273587
#> Values[k8].InitialValue -3.426533089 -0.0964735315
#> Values[kdnc].InitialValue -0.033423018 -0.0032234487
#> Values[Kd].InitialValue Values[Kdp].InitialValue
#> Values[vmP].InitialValue 9.441290e-04 2.462906e-05
#> Values[kdmp].InitialValue 5.430144e-04 -4.407883e-03
#> Values[KAP].InitialValue -1.680887e-03 4.014793e-03
#> Values[KmP].InitialValue -8.216578e-03 5.221407e-02
#> Values[vmC].InitialValue 1.547780e-03 -1.124316e-02
#> Values[kdmc].InitialValue 7.509288e-04 -4.282797e-03
#> Values[KAC].InitialValue 1.635511e-05 -1.472607e-03
#> Values[KmC].InitialValue -2.427384e-03 1.471488e-02
#> Values[vmB].InitialValue 3.454270e-03 -2.189789e-02
#> Values[kdmb].InitialValue 2.727546e-04 -1.693490e-03
#> Values[KIB].InitialValue 1.075426e-02 -1.004314e-01
#> Values[KmB].InitialValue -5.567041e-02 3.644737e-01
#> Values[k1].InitialValue 5.421195e-06 2.997637e-04
#> Values[k2].InitialValue -1.110065e-02 5.822085e-02
#> Values[k3].InitialValue 9.134001e-03 -4.577389e-02
#> Values[k4].InitialValue -1.197388e-02 5.093730e-03
#> Values[k5].InitialValue 6.711124e-04 -9.988636e-03
#> Values[k6].InitialValue 1.044643e-03 -9.199851e-03
#> Values[k7].InitialValue -4.095996e-02 2.401285e-01
#> Values[k8].InitialValue -2.724026e-02 1.623180e-01
#> Values[kdnc].InitialValue -8.402471e-04 4.715819e-03
#> Values[Kp].InitialValue Values[Vphos].InitialValue
#> Values[vmP].InitialValue -1.689635e-03 1.849401e-04
#> Values[kdmp].InitialValue -2.322926e-03 9.121099e-04
#> Values[KAP].InitialValue 2.524297e-03 -1.246776e-03
#> Values[KmP].InitialValue 2.572162e-02 -1.026024e-02
#> Values[vmC].InitialValue -6.141154e-03 2.339791e-03
#> Values[kdmc].InitialValue -2.365979e-03 8.100724e-04
#> Values[KAC].InitialValue 2.709412e-05 1.951036e-04
#> Values[KmC].InitialValue 9.098553e-03 -3.638480e-03
#> Values[vmB].InitialValue -1.126356e-02 4.875636e-03
#> Values[kdmb].InitialValue -8.327923e-04 3.659444e-04
#> Values[KIB].InitialValue -6.836245e-02 2.636870e-02
#> Values[KmB].InitialValue 1.922818e-01 -8.219219e-02
#> Values[k1].InitialValue -7.008600e-04 3.977147e-05
#> Values[k2].InitialValue 3.052378e-02 -1.394238e-02
#> Values[k3].InitialValue -2.130375e-02 9.539211e-03
#> Values[k4].InitialValue -1.706720e-03 -1.994457e-03
#> Values[k5].InitialValue -4.306907e-03 2.103232e-03
#> Values[k6].InitialValue -3.438652e-03 1.819004e-03
#> Values[k7].InitialValue 1.213663e-01 -5.191061e-02
#> Values[k8].InitialValue 7.795059e-02 -3.504186e-02
#> Values[kdnc].InitialValue 2.405585e-03 -8.330632e-04
#> Values[V1B].InitialValue Values[V1C].InitialValue
#> Values[vmP].InitialValue -0.0012935348 0.008046290
#> Values[kdmp].InitialValue -0.0015673842 0.009861355
#> Values[KAP].InitialValue 0.0015542087 -0.011143817
#> Values[KmP].InitialValue 0.0191434044 -0.116877931
#> Values[vmC].InitialValue -0.0042739285 0.027062012
#> Values[kdmc].InitialValue -0.0017005524 0.010736545
#> Values[KAC].InitialValue -0.0003669680 -0.001187301
#> Values[KmC].InitialValue 0.0068584815 -0.041950942
#> Values[vmB].InitialValue -0.0082722237 0.049874793
#> Values[kdmb].InitialValue -0.0006211625 0.003742148
#> Values[KIB].InitialValue -0.0473655402 0.289270212
#> Values[KmB].InitialValue 0.1401350120 -0.844453057
#> Values[k1].InitialValue -0.0000937286 0.001014750
#> Values[k2].InitialValue 0.0232327817 -0.138382283
#> Values[k3].InitialValue -0.0159551108 0.097223739
#> Values[k4].InitialValue 0.0004578370 0.011785936
#> Values[k5].InitialValue -0.0035355236 0.020771748
#> Values[k6].InitialValue -0.0023161146 0.015375070
#> Values[k7].InitialValue 0.0881303652 -0.527509253
#> Values[k8].InitialValue 0.0552023789 -0.339663851
#> Values[kdnc].InitialValue 0.0017919421 -0.011984332
#> Values[V2B].InitialValue Values[V2C].InitialValue
#> Values[vmP].InitialValue 7.623156e-04 0.012908332
#> Values[kdmp].InitialValue 5.009783e-04 0.018707965
#> Values[KAP].InitialValue 2.337544e-04 -0.021458146
#> Values[KmP].InitialValue -9.288457e-03 -0.213502820
#> Values[vmC].InitialValue 1.795522e-03 0.049164950
#> Values[kdmc].InitialValue 6.062570e-04 0.018601342
#> Values[KAC].InitialValue 9.008230e-04 0.001567361
#> Values[KmC].InitialValue -4.330029e-03 -0.076894918
#> Values[vmB].InitialValue 3.550186e-03 0.092697103
#> Values[kdmb].InitialValue 2.641416e-04 0.006965007
#> Values[KIB].InitialValue 2.303340e-02 0.525865159
#> Values[KmB].InitialValue -6.029040e-02 -1.567311047
#> Values[k1].InitialValue 9.067647e-05 0.002768138
#> Values[k2].InitialValue -1.033873e-02 -0.257209297
#> Values[k3].InitialValue 5.719480e-03 0.176188310
#> Values[k4].InitialValue -1.766556e-03 0.007230667
#> Values[k5].InitialValue 2.674320e-03 0.037659310
#> Values[k6].InitialValue 9.611723e-04 0.028794185
#> Values[k7].InitialValue -3.613116e-02 -0.984228344
#> Values[k8].InitialValue 3.163777e-03 -0.627124205
#> Values[kdnc].InitialValue -7.859350e-04 -0.019067066
#> Values[V2P].InitialValue Values[V2PC].InitialValue
#> Values[vmP].InitialValue 0.006413576 0.0030132547
#> Values[kdmp].InitialValue 0.008616843 0.0013083473
#> Values[KAP].InitialValue -0.011119174 -0.0015745878
#> Values[KmP].InitialValue -0.099989167 -0.0202599161
#> Values[vmC].InitialValue 0.023735722 0.0038152562
#> Values[kdmc].InitialValue 0.008424367 0.0022314123
#> Values[KAC].InitialValue -0.001129459 0.0017038612
#> Values[KmC].InitialValue -0.035357615 -0.0079058739
#> Values[vmB].InitialValue 0.042825793 0.0090008036
#> Values[kdmb].InitialValue 0.003188429 0.0006304260
#> Values[KIB].InitialValue 0.250330890 0.0640289855
#> Values[KmB].InitialValue -0.726922024 -0.1586523144
#> Values[k1].InitialValue 0.002173196 -0.0013735732
#> Values[k2].InitialValue -0.123307423 -0.0249391428
#> Values[k3].InitialValue 0.080627756 0.0161400127
#> Values[k4].InitialValue 0.006558810 0.0132190810
#> Values[k5].InitialValue 0.016598170 0.0055485961
#> Values[k6].InitialValue 0.011895694 0.0045395148
#> Values[k7].InitialValue -0.454892838 -0.0900845920
#> Values[k8].InitialValue -0.284022524 -0.0619777097
#> Values[kdnc].InitialValue -0.008592753 -0.0017233145
#> Values[V3B].InitialValue Values[V4B].InitialValue
#> Values[vmP].InitialValue 0.0042080665 1.370592e-03
#> Values[kdmp].InitialValue 0.0058760963 -5.302983e-04
#> Values[KAP].InitialValue -0.0065356720 7.385265e-04
#> Values[KmP].InitialValue -0.0682771955 4.487689e-03
#> Values[vmC].InitialValue 0.0157028447 -7.872808e-04
#> Values[kdmc].InitialValue 0.0060692531 -3.899043e-04
#> Values[KAC].InitialValue 0.0001647663 2.720735e-05
#> Values[KmC].InitialValue -0.0249026837 4.975907e-04
#> Values[vmB].InitialValue 0.0295543064 -2.644792e-03
#> Values[kdmb].InitialValue 0.0022092803 -2.224484e-04
#> Values[KIB].InitialValue 0.1725527681 -1.309143e-02
#> Values[KmB].InitialValue -0.5013902060 4.220815e-02
#> Values[k1].InitialValue 0.0007717008 1.447926e-05
#> Values[k2].InitialValue -0.0834275214 5.246157e-03
#> Values[k3].InitialValue 0.0553247182 -5.309756e-03
#> Values[k4].InitialValue 0.0003510345 8.414038e-03
#> Values[k5].InitialValue 0.0118444049 -1.410603e-03
#> Values[k6].InitialValue 0.0081331693 -1.305798e-03
#> Values[k7].InitialValue -0.3152691262 3.090544e-02
#> Values[k8].InitialValue -0.1948834412 2.317422e-02
#> Values[kdnc].InitialValue -0.0062954617 9.731323e-04
#> Values[V4PC].InitialValue Values[vdBC].InitialValue
#> Values[vmP].InitialValue -0.0233239710 -0.012109507
#> Values[kdmp].InitialValue -0.0275960801 -0.005844249
#> Values[KAP].InitialValue 0.0286589293 0.015755766
#> Values[KmP].InitialValue 0.3313004342 0.138122578
#> Values[vmC].InitialValue -0.0742486255 -0.035823312
#> Values[kdmc].InitialValue -0.0302930358 -0.013548851
#> Values[KAC].InitialValue -0.0040311500 0.026792773
#> Values[KmC].InitialValue 0.1192468102 0.013080451
#> Values[vmB].InitialValue -0.1422455203 -0.052888739
#> Values[kdmb].InitialValue -0.0105923394 -0.004291050
#> Values[KIB].InitialValue -0.8351794613 -0.325159255
#> Values[KmB].InitialValue 2.4162984706 0.855146854
#> Values[k1].InitialValue -0.0009238571 -0.021143800
#> Values[k2].InitialValue 0.3988206093 0.132029327
#> Values[k3].InitialValue -0.2709650609 -0.167397436
#> Values[k4].InitialValue -0.0118381494 -0.152304155
#> Values[k5].InitialValue -0.0570791256 -0.007433783
#> Values[k6].InitialValue -0.0418315004 0.001205591
#> Values[k7].InitialValue 1.5043975043 0.510967277
#> Values[k8].InitialValue 0.9541151203 0.216056538
#> Values[kdnc].InitialValue 0.0304053507 0.016569705
#> Values[vdBN].InitialValue Values[vdCC].InitialValue
#> Values[vmP].InitialValue -0.0054789146 -0.004253473
#> Values[kdmp].InitialValue -0.0055809172 -0.004976497
#> Values[KAP].InitialValue 0.0094883209 0.005850134
#> Values[KmP].InitialValue 0.0541763186 0.059231602
#> Values[vmC].InitialValue -0.0137270923 -0.012345103
#> Values[kdmc].InitialValue -0.0065140323 -0.003992791
#> Values[KAC].InitialValue 0.0058866914 -0.003612633
#> Values[KmC].InitialValue 0.0212667686 0.023221759
#> Values[vmB].InitialValue -0.0240156654 -0.025454274
#> Values[kdmb].InitialValue -0.0018262090 -0.001891768
#> Values[KIB].InitialValue -0.1508041530 -0.150746705
#> Values[KmB].InitialValue 0.4044641299 0.434536627
#> Values[k1].InitialValue -0.0036990523 -0.001280318
#> Values[k2].InitialValue 0.0598927977 0.072830728
#> Values[k3].InitialValue -0.0298334246 -0.047377880
#> Values[k4].InitialValue 0.0064533259 0.005419520
#> Values[k5].InitialValue -0.0065692534 -0.010690456
#> Values[k6].InitialValue -0.0063115109 -0.005476985
#> Values[k7].InitialValue 0.2558731583 0.266991245
#> Values[k8].InitialValue 0.1351233462 0.173936658
#> Values[kdnc].InitialValue 0.0084197221 0.002007804
#> Values[vdIN].InitialValue Values[vdPC].InitialValue
#> Values[vmP].InitialValue 0.017740501 -9.882288e-04
#> Values[kdmp].InitialValue 0.014431770 -1.136973e-03
#> Values[KAP].InitialValue -0.014549178 5.946363e-04
#> Values[KmP].InitialValue -0.193050251 2.998121e-02
#> Values[vmC].InitialValue 0.044159170 -5.222519e-03
#> Values[kdmc].InitialValue 0.022127757 -2.874444e-03
#> Values[KAC].InitialValue -0.007460657 2.004022e-04
#> Values[KmC].InitialValue -0.051231790 5.995573e-03
#> Values[vmB].InitialValue 0.076252686 -1.119229e-02
#> Values[kdmb].InitialValue 0.005941764 -8.356453e-04
#> Values[KIB].InitialValue 0.396131756 -8.214434e-02
#> Values[KmB].InitialValue -1.274084663 1.912991e-01
#> Values[k1].InitialValue -0.012616000 1.132619e-03
#> Values[k2].InitialValue -0.201423256 3.276954e-02
#> Values[k3].InitialValue 0.168942091 -2.070627e-02
#> Values[k4].InitialValue 0.003755973 4.031427e-03
#> Values[k5].InitialValue 0.036181320 -3.677002e-03
#> Values[k6].InitialValue 0.016818597 -3.376537e-03
#> Values[k7].InitialValue -0.845796533 1.163499e-01
#> Values[k8].InitialValue -0.440138261 1.065522e-01
#> Values[kdnc].InitialValue -0.027426214 3.532267e-03
#> Values[vdPCC].InitialValue Values[vdPCN].InitialValue
#> Values[vmP].InitialValue 0.0025012774 2.551235e-04
#> Values[kdmp].InitialValue 0.0047491914 -1.206112e-03
#> Values[KAP].InitialValue -0.0062608687 -1.383645e-03
#> Values[KmP].InitialValue -0.0501240255 -1.173265e-02
#> Values[vmC].InitialValue 0.0125255446 -1.270760e-03
#> Values[kdmc].InitialValue 0.0045860017 8.040371e-04
#> Values[KAC].InitialValue -0.0013668098 1.803948e-03
#> Values[KmC].InitialValue -0.0175022422 3.569239e-03
#> Values[vmB].InitialValue 0.0222046454 3.754089e-03
#> Values[kdmb].InitialValue 0.0016757915 3.167571e-04
#> Values[KIB].InitialValue 0.1295885618 9.885311e-03
#> Values[KmB].InitialValue -0.3736432318 -5.705298e-02
#> Values[k1].InitialValue 0.0007412429 -2.425044e-03
#> Values[k2].InitialValue -0.0658037129 -1.179346e-02
#> Values[k3].InitialValue 0.0444574398 7.057153e-03
#> Values[k4].InitialValue 0.0158908112 -6.487370e-02
#> Values[k5].InitialValue 0.0089643368 -3.009275e-03
#> Values[k6].InitialValue 0.0065434740 2.453085e-03
#> Values[k7].InitialValue -0.2368821634 -3.913001e-02
#> Values[k8].InitialValue -0.1515363575 -2.690512e-02
#> Values[kdnc].InitialValue -0.0052840400 -1.234632e-03
#> [ erreichte getOption("max.print") -- 25 Zeilen ausgelassen ]
add_pe_param_global <- function(name, upper, lower){
value <- getGlobalQuantities(key = name)$initial_value
value_ref <- getGlobalQuantityReferences(key = name)$initial_value
addParameterEstimationParameter( ref = value_ref,
start_value = value,
lower_bound = value-value*lower,
upper_bound = value+value*upper)
}